2 Answers
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Tile layouts are stored in a file called appsFolder.itemdata-ms located in C:\Users\%username%\AppData\Roaming\Microsoft\Windows.

Basically, you can arrange the tiles however you want then take a copy of this file and place it the default user profile (either manually or in your build). New users logging in will then get this pre-defined tile configuration.

You can also copy it directly to the user profile and it will reset the configuration next time the user logs in.

With the recent updates to the Group Policies, you do have a lot of flexibility with the different options of the Metro Apps and Start Menu. Check out this link for reference on how to handle the different options.

Some features even include removing or blocking specified apps (including the store).